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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1239/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetMashR 1.0.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MetMashR
git_branch: RELEASE_3_20
git_last_commit: 5ccb773
git_last_commit_date: 2024-10-29 11:34:47 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for MetMashR on nebbiolo2

To the developers/maintainers of the MetMashR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetMashR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MetMashR
Version: 1.0.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MetMashR_1.0.0.tar.gz
StartedAt: 2024-12-20 02:32:50 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:43:59 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 669.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MetMashR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MetMashR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MetMashR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MetMashR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetMashR’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/PE%2816%3A0_18%3A1%29/inchi_key%2Chmdb_id/json.json
  MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/TG%2816%3A0_16%3A1_18%3A2%29/inchi_key%2Chmdb_id/json.json
  MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/TG%2816%3A0_16%3A1_18%3A2%29/inchi_key%2Chmdb_id

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MetMashR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MetMashR.Rcheck/00check.log’
for details.


Installation output

MetMashR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MetMashR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘MetMashR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MetMashR)

Tests output

MetMashR.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(MetMashR)
Loading required package: struct
> 
> test_check("MetMashR")
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 249 ]
> 
> proc.time()
   user  system elapsed 
 13.466   0.852  23.317 

Example timings

MetMashR.Rcheck/MetMashR-Ex.timings

nameusersystemelapsed
AnnotationDb_database0.0210.0000.021
AnnotationDb_select0.0110.0000.012
BiocFileCache_database0.0160.0000.016
CompoundDb_source0.0090.0010.010
GO_database0.0100.0020.011
MTox700plus_database0.0200.0010.021
PathBank_metabolite_database0.0220.0030.025
add_columns0.0090.0010.009
add_labels0.0070.0030.010
annotation_bar_chart0.0070.0010.010
annotation_database0.0070.0020.009
annotation_histogram0.0110.0010.013
annotation_histogram2d0.0100.0020.013
annotation_pie_chart0.0120.0020.015
annotation_source0.0080.0000.008
annotation_table0.0100.0000.011
annotation_upset_chart0.0150.0010.017
annotation_venn_chart0.0120.0000.013
cache_as_is0.0250.0060.031
calc_ppm_diff0.0070.0000.008
calc_rt_diff0.0050.0020.008
cd_source0.0140.0030.016
chart_plot0.0100.0010.012
check_for_columns0.0120.0020.013
classyfire_lookup0.0130.0030.017
combine_columns0.0090.0020.012
combine_records0.0070.0010.009
combine_records_helper_functions0.0410.0110.052
combine_sources0.0400.0000.041
compute_column0.0070.0000.007
compute_record0.0040.0000.005
database_lookup0.0110.0000.011
eutils_lookup0.0150.0000.015
excel_database0.0140.0000.014
filter_labels0.0090.0000.009
filter_na0.0050.0000.005
filter_range0.0080.0000.008
filter_records0.0060.0000.006
filter_venn0.0110.0000.011
github_file0.020.000.02
greek_dictionary0.0080.0000.008
hmdb_lookup0.0110.0000.013
id_counts0.0060.0000.006
import_source000
is_writable0.0140.0000.014
kegg_lookup0.0070.0000.007
lcms_table0.0120.0000.012
lipidmaps_lookup0.0150.0000.014
ls_source0.0120.0000.012
model_apply0.1540.0000.154
mspurity_source0.0080.0000.009
mwb_compound_lookup0.0130.0000.014
mwb_refmet_database0.0100.0010.011
mwb_structure0.0070.0000.007
mz_match0.0080.0000.008
mzrt_match0.010.000.01
normalise_lipids0.0080.0000.008
normalise_strings0.0110.0000.012
openbabel_structure0.0140.0000.014
opsin_lookup0.0120.0000.012
pivot_columns0.0060.0000.007
prioritise_columns0.0090.0000.009
pubchem_compound_lookup0.0120.0000.013
pubchem_property_lookup0.0140.0000.014
pubchem_structure0.0070.0000.008
pubchem_widget0.0120.0000.013
racemic_dictionary0.0050.0010.006
rdata_database0.0090.0000.010
rds_cache0.0080.0000.009
rds_database0.0080.0000.008
read_database0.0180.0000.018
read_source0.0330.0000.033
remove_columns0.0050.0000.005
rename_columns0.0060.0000.006
required_cols0.0170.0110.030
rest_api0.0120.0010.014
rt_match0.0060.0030.009
select_columns0.0050.0000.006
split_column0.0090.0010.011
split_records0.0080.0010.009
sqlite_database0.0090.0030.012
trim_whitespace0.0050.0000.007
tripeptide_dictionary0.0070.0000.007
unique_records0.0010.0010.001
unzip_before_cache0.0120.0000.013
vertical_join0.1240.0150.139
wherever0.0360.0000.036
write_database0.0050.0000.005